BM HCA MPAL transfer label

This vignette will show basic functions provided by viewmaster

#load greenleaf MPAL dataset into monocle3

mpal<-readRDS(file ="/Volumes/fh/fast/furlan_s/grp/data/ddata/BM_data/healthy_bone_marrow_greenleaf.rds")
plot_cells(mpal, color_cells_by = "BioClassification", label_cell_groups = F)+scale_color_manual(values = sfc(n = 26))

#load hca bone marrow seurat object, convert to monocle using viewmaster’s helpful function

hca<-readRDS(file = "/Volumes/fh/fast/furlan_s/grp/data/ddata/BM_data/palantir_bm_r1.rds")
hca<-seurat_to_monocle3(hca, seu_rd = "tsne")
plot_cells(hca , color_cells_by = "cell_annotation", label_cell_groups = F)+scale_color_manual(values = sfc(10, scramble = F))

#Detect common variant genes between two cell data sets

vg<-common_variant_genes(mpal, hca, top_n = 5000)

vg

##    [1] "LINC00115"    "FAM41C"       "ISG15"        "TNFRSF18"    
##    [5] "TNFRSF4"      "CCNL2"        "TTC34"        "SMIM1"       
##    [9] "THAP3"        "PER3"         "TNFRSF9"      "SLC2A5"      
##   [13] "NMNAT1"       "CASZ1"        "FBXO44"       "DRAXIN"      
##   [17] "PRDM2"        "DNAJC16"      "FBLIM1"       "PADI4"       
##   [21] "TMCO4"        "C1QB"         "ID3"          "CNR2"        
##   [25] "RCAN3"        "RUNX3"        "PAFAH2"       "CNKSR1"      
##   [29] "CD52"         "ZNF683"       "TMEM222"      "SYTL1"       
##   [33] "AHDC1"        "IFI6"         "PTAFR"        "GMEB1"       
##   [37] "LCK"          "MARCKSL1"     "FAM229A"      "ZBTB8A"      
##   [41] "SYNC"         "CSF3R"        "SNIP1"        "INPP5B"      
##   [45] "RLF"          "COL9A2"       "EXO5"         "RIMS3"       
##   [49] "SCMH1"        "FOXO6"        "HIVEP3"       "CCDC30"      
##   [53] "SZT2"         "UROD"         "MOB3C"        "PDZK1IP1"    
##   [57] "BEND5"        "CC2D1B"       "ECHDC2"       "TCEANC2"     
##   [61] "ACOT11"       "TTC22"        "OMA1"         "JUN"         
##   [65] "EFCAB7"       "LEPR"         "LEPROT"       "PDE4B"       
##   [69] "SLC35D1"      "LRRC7"        "ANKRD13C"     "HHLA3"       
##   [73] "NEGR1"        "CRYZ"         "GIPC2"        "IFI44L"      
##   [77] "PRKACB"       "BCL10"        "ODF2L"        "LMO4"        
##   [81] "GBP3"         "GBP1"         "GBP2"         "GBP4"        
##   [85] "LRRC8B"       "LRRC8C"       "TGFBR3"       "FAM69A"      
##   [89] "CNN3"         "RWDD3"        "PTBP2"        "TRMT13"      
##   [93] "DBT"          "S1PR1"        "VAV3"         "CYB561D1"    
##   [97] "CSF1"         "SLC16A4"      "KCNA3"        "CEPT1"       
##  [101] "WNT2B"        "MOV10"        "RHOC"         "PPM1J"       
##  [105] "LRIG2"        "PHTF1"        "TSPAN2"       "CD2"         
##  [109] "PDE4DIP"      "ITGA10"       "NUDT17"       "NBPF12"      
##  [113] "PRKAB2"       "HIST2H2BF"    "HIST2H2BE"    "HIST2H2AB"   
##  [117] "MCL1"         "CTSS"         "CDC42SE1"     "S100A11"     
##  [121] "S100A12"      "ATP8B2"       "PBXIP1"       "EFNA4"       
##  [125] "EFNA1"        "SLC50A1"      "TRIM46"       "LMNA"        
##  [129] "FCRL5"        "FCRL2"        "SPTA1"        "MNDA"        
##  [133] "FCER1A"       "IGSF8"        "PEX19"        "SLAMF7"      
##  [137] "LY9"          "FCER1G"       "FCRLA"        "PBX1"        
##  [141] "POU2F1"       "CD247"        "RCSD1"        "MPC2"        
##  [145] "ATP1B1"       "SELP"         "SELL"         "SCYL3"       
##  [149] "VAMP4"        "DNM3"         "KLHL20"       "ZBTB37"      
##  [153] "KIAA0040"     "RALGPS2"      "ABL2"         "LHX4"        
##  [157] "IER5"         "RNASEL"       "NCF2"         "SWT1"        
##  [161] "PTGS2"        "RGS18"        "RGS1"         "CFH"         
##  [165] "ZBTB41"       "MIR181A1HG"   "ZNF281"       "NAV1"        
##  [169] "LGR6"         "LAX1"         "ZBED6"        "PIK3C2B"     
##  [173] "DSTYK"        "TMCC2"        "NUAK2"        "SLC45A3"     
##  [177] "NUCKS1"       "SLC41A1"      "CD55"         "CD34"        
##  [181] "TRAF3IP3"     "TRAF5"        "VASH2"        "PTPN14"      
##  [185] "BPNT1"        "AIDA"         "ENAH"         "TMEM63A"     
##  [189] "ZNF678"       "JMJD4"        "IBA57"        "OBSCN"       
##  [193] "FAM89A"       "SPRTN"        "TARBP1"       "GGPS1"       
##  [197] "LYST"         "GPR137B"      "CHRM3"        "AKT3"        
##  [201] "ZBTB18"       "CNST"         "ZNF669"       "GCSAML"      
##  [205] "PGBD2"        "SH3YL1"       "PXDN"         "RSAD2"       
##  [209] "ID2"          "LPIN1"        "TRIB2"        "LINC00954"   
##  [213] "RHOB"         "DNAJC27"      "POMC"         "DNMT3A"      
##  [217] "FOSL2"        "LBH"          "LCLAT1"       "LTBP1"       
##  [221] "RASGRP3"      "CRIM1"        "CYP1B1"       "GALM"        
##  [225] "MTA3"         "ZFP36L2"      "PLEKHH2"      "PRKCE"       
##  [229] "ATP6V1E2"     "SOCS5"        "EPCAM"        "KCNK12"      
##  [233] "CLHC1"        "LINC01122"    "BCL11A"       "WDPCP"       
##  [237] "PELI1"        "CEP68"        "MEIS1"        "CNRIP1"      
##  [241] "PLEK"         "ARHGAP25"     "GFPT1"        "AAK1"        
##  [245] "PAIP2B"       "RAB11FIP5"    "CCDC142"      "ELMOD3"      
##  [249] "CAPG"         "ST3GAL5"      "EIF2AK3"      "ZNF2"        
##  [253] "ARID5A"       "FAM178B"      "ZAP70"        "INPP4A"      
##  [257] "TSGA10"       "LIPT1"        "LYG2"         "AFF3"        
##  [261] "IL18R1"       "TMEM182"      "FHL2"         "NCK2"        
##  [265] "GCC2"         "LIMS1"        "RGPD5"        "ZC3H6"       
##  [269] "IL1B"         "CCDC93"       "PTPN4"        "BIN1"        
##  [273] "ARHGEF4"      "RAB3GAP1"     "CXCR4"        "GTDC1"       
##  [277] "ZEB2"         "RBM43"        "NR4A2"        "CYTIP"       
##  [281] "ACVR1C"       "IFIH1"        "COBLL1"       "SCN3A"       
##  [285] "SCN9A"        "TTC30B"       "CWC22"        "ITGA4"       
##  [289] "FSIP2"        "TFPI"         "SLC40A1"      "ANKRD44"     
##  [293] "TYW5"         "KCTD18"       "FAM126B"      "BMPR2"       
##  [297] "CARF"         "CYP20A1"      "ABI2"         "INO80D"      
##  [301] "ZDBF2"        "KLF7"         "PLEKHM3"      "CRYGD"       
##  [305] "CPS1"         "IKZF2"        "FN1"          "IGFBP2"      
##  [309] "RNF25"        "ANKZF1"       "DNAJB2"       "CHPF"        
##  [313] "DOCK10"       "FBXO36"       "SP140L"       "ITM2C"       
##  [317] "NPPC"         "DIS3L2"       "TIGD1"        "SAG"         
##  [321] "DGKD"         "ARL4C"        "COL6A3"       "RAMP1"       
##  [325] "DUSP28"       "SNED1"        "ITPR1"        "SRGAP3"      
##  [329] "TTLL3"        "CRELD1"       "PRRT3"        "IRAK2"       
##  [333] "IQSEC1"       "XPC"          "CCDC174"      "CAPN7"       
##  [337] "SH3BP5"       "METTL6"       "COLQ"         "ANKRD28"     
##  [341] "PLCL2"        "SATB1"        "ZNF385D"      "NKIRAS1"     
##  [345] "TOP2B"        "TGFBR2"       "OSBPL10"      "CMTM8"       
##  [349] "CMTM7"        "ARPP21"       "TRANK1"       "EPM2AIP1"    
##  [353] "VILL"         "PLCD1"        "EXOG"         "TTC21A"      
##  [357] "CSRNP1"       "SNRK"         "ZNF852"       "ZNF197"      
##  [361] "TMEM42"       "LIMD1"        "ALS2CL"       "NBEAL2"      
##  [365] "CAMP"         "TCTA"         "IP6K1"        "MANF"        
##  [369] "DNAH1"        "ITIH4"        "TKT"          "CCDC66"      
##  [373] "ARHGEF3"      "DENND6A"      "FLNB"         "DNASE1L3"    
##  [377] "SLC25A26"     "LRIG1"        "SUCLG2"       "LMOD3"       
##  [381] "FOXP1"        "EBLN2"        "HTR1F"        "ZNF654"      
##  [385] "NSUN3"        "CLDND1"       "SENP7"        "NFKBIZ"      
##  [389] "CBLB"         "DZIP3"        "DPPA4"        "CD96"        
##  [393] "PHLDB2"       "GCSAM"        "CD200"        "SIDT1"       
##  [397] "GRAMD1C"      "ZBTB20"       "POPDC2"       "CSTA"        
##  [401] "WDR5B"        "PARP14"       "MYLK"         "KALRN"       
##  [405] "PLXNA1"       "GATA2"        "GP9"          "HMCES"       
##  [409] "H1FX"         "ASTE1"        "ACAD11"       "EPHB1"       
##  [413] "SLC9A9"       "CPA3"         "TM4SF1"       "PFN2"        
##  [417] "TSC22D2"      "MED12L"       "GPR171"       "P2RY14"      
##  [421] "IGSF10"       "SUCNR1"       "ARHGEF26"     "MME"         
##  [425] "SLC33A1"      "IFT80"        "SERPINI1"     "MYNN"        
##  [429] "PHC3"         "SKIL"         "TNFSF10"      "ZMAT3"       
##  [433] "PIK3CA"       "MFN1"         "ATP11B"       "KLHL24"      
##  [437] "MAGEF1"       "VPS8"         "LPP"          "CCDC50"      
##  [441] "FAM43A"       "MUC20"        "TFRC"         "WDR53"       
##  [445] "DLG1"         "LRCH3"        "ZNF595"       "ZNF721"      
##  [449] "PDE6B"        "RNF212"       "UVSSA"        "TMEM129"     
##  [453] "RGS12"        "ZBTB49"       "CYTL1"        "CRMP1"       
##  [457] "TADA2B"       "SH3TC1"       "ZNF518B"      "CLNK"        
##  [461] "HS3ST1"       "CD38"         "PROM1"        "TAPT1"       
##  [465] "FAM184B"      "SEPSECS"      "PI4K2B"       "SEL1L3"      
##  [469] "TBC1D19"      "STIM2"        "ARAP2"        "TLR10"       
##  [473] "SMIM14"       "RHOH"         "ATP8A1"       "GNPDA2"      
##  [477] "ATP10D"       "TXK"          "SGCB"         "LNX1"        
##  [481] "CLOCK"        "NMU"          "HOPX"         "SPINK2"      
##  [485] "STAP1"        "COX18"        "RASSF6"       "PF4"         
##  [489] "PPBP"         "CXCL3"        "CXCL2"        "AREG"        
##  [493] "THAP6"        "CXCL10"       "CNOT6L"       "ANTXR2"      
##  [497] "PLAC8"        "HELQ"         "ARHGAP24"     "PTPN13"      
##  [501] "ABCG2"        "PPM1K"        "HERC5"        "NAP1L5"      
##  [505] "GPRIN3"       "MMRN1"        "HPGDS"        "DAPP1"       
##  [509] "EMCN"         "BANK1"        "SLC9B1"       "TBCK"        
##  [513] "CYP2U1"       "LEF1"         "TIFA"         "SNHG8"       
##  [517] "USP53"        "SPRY1"        "MFSD8"        "RAB33B"      
##  [521] "INPP4B"       "GAB1"         "GYPB"         "HHIP"        
##  [525] "SMAD1"        "ZNF827"       "LRBA"         "TMEM154"     
##  [529] "TRIM2"        "TLR2"         "RNF175"       "FAM198B"     
##  [533] "MARCH1"       "TMEM192"      "CBR4"         "CLCN3"       
##  [537] "FBXO8"        "HPGD"         "CDKN2AIP"     "SNX25"       
##  [541] "LRP2BP"       "UFSP2"        "LPCAT1"       "BASP1"       
##  [545] "NPR3"         "SPEF2"        "IL7R"         "RICTOR"      
##  [549] "DAB2"         "PTGER4"       "CCDC152"      "ANXA2R"      
##  [553] "PARP8"        "SNX18"        "GZMK"         "SLC38A9"     
##  [557] "IL6ST"        "MIER3"        "GAPT"         "PDE4D"       
##  [561] "PPWD1"        "TRIM23"       "TRAPPC13"     "SGTB"        
##  [565] "MAST4"        "CD180"        "PIK3R1"       "SERF1A"      
##  [569] "GTF2H2"       "PTCD2"        "ANKRA2"       "F2R"         
##  [573] "CRHBP"        "SERINC5"      "DHFR"         "SSBP2"       
##  [577] "VCAN"         "MEF2C"        "FAM172A"      "POU5F2"      
##  [581] "GLRX"         "GIN1"         "NREP"         "EPB41L4A-AS1"
##  [585] "LOX"          "SNX2"         "CSNK1G3"      "ZNF608"      
##  [589] "MARCH3"       "RAPGEF6"      "ACSL6"        "P4HA2"       
##  [593] "IRF1"         "KIF3A"        "LEAP2"        "ZCCHC10"     
##  [597] "TCF7"         "CDKL3"        "JADE2"        "TGFBI"       
##  [601] "KLHL3"        "EGR1"         "MZB1"         "CXXC5"       
##  [605] "HBEGF"        "ANKHD1"       "GNPDA1"       "HMHB1"       
##  [609] "CSF1R"        "TCOF1"        "IRGM"         "ITK"         
##  [613] "CYFIP2"       "ADAM19"       "EBF1"         "HMMR"        
##  [617] "CREBRF"       "SFXN1"        "HRH2"         "FAM153B"     
##  [621] "SIMC1"        "TSPAN17"      "ZNF346"       "MXD3"        
##  [625] "PRR7"         "DBN1"         "N4BP3"        "RMND5B"      
##  [629] "PHYKPL"       "CLK4"         "ZNF354B"      "ZFP62"       
##  [633] "TRIM41"       "TRIM52"       "IRF4"         "SERPINB1"    
##  [637] "SERPINB9"     "SLC22A23"     "F13A1"        "LY86"        
##  [641] "SLC35B3"      "TMEM14C"      "HIVEP1"       "PHACTR1"     
##  [645] "GFOD1"        "SIRT5"        "MYLIP"        "SOX4"        
##  [649] "CASC15"       "GPLD1"        "ALDH5A1"      "HIST1H1C"    
##  [653] "HIST1H2BC"    "HIST1H2AC"    "HIST1H2BD"    "HIST1H2BF"   
##  [657] "HIST1H4E"     "HIST1H2BG"    "HIST1H2AE"    "HIST1H1D"    
##  [661] "HIST1H4H"     "BTN3A2"       "BTN2A2"       "BTN3A1"      
##  [665] "BTN3A3"       "BTN2A1"       "HIST1H2BJ"    "ZNF184"      
##  [669] "HIST1H2BN"    "HIST1H1B"     "ZSCAN16"      "GABBR1"      
##  [673] "HLA-F"        "TRIM39"       "PPP1R10"      "IER3"        
##  [677] "DDR1"         "TNF"          "LTB"          "LST1"        
##  [681] "DDAH2"        "HSPA1A"       "DXO"          "AGER"        
##  [685] "HLA-DRB5"     "HLA-DRB1"     "HLA-DQA1"     "HLA-DQA2"    
##  [689] "HLA-DQB2"     "HLA-DOB"      "HLA-DMB"      "HLA-DMA"     
##  [693] "HLA-DPB1"     "RXRB"         "B3GALT4"      "RGL2"        
##  [697] "ZBTB22"       "PHF1"         "ITPR3"        "LEMD2"       
##  [701] "PACSIN1"      "STK38"        "FGD2"         "KCNK17"      
##  [705] "TFEB"         "TRERF1"       "PTCRA"        "PEX6"        
##  [709] "KLC4"         "TJAP1"        "SUPT3H"       "RUNX2"       
##  [713] "ENPP4"        "TNFRSF21"     "EFHC1"        "GSTA4"       
##  [717] "ICK"          "LRRC1"        "B3GAT2"       "OGFRL1"      
##  [721] "DDX43"        "MTO1"         "SLC17A5"      "TPBG"        
##  [725] "BACH2"        "FBXL4"        "QRSL1"        "SCML4"       
##  [729] "OSTM1"        "AK9"          "WASF1"        "TRAF3IP2"    
##  [733] "KPNA5"        "CEP85L"       "NKAIN2"       "SAMD3"       
##  [737] "TMEM200A"     "LINC01013"    "STX7"         "SGK1"        
##  [741] "MYB"          "PDE7B"        "TNFAIP3"      "HECA"        
##  [745] "CITED2"       "HIVEP2"       "RAB32"        "UST"         
##  [749] "ZC3H12D"      "AKAP12"       "ZBTB2"        "SYNE1"       
##  [753] "MYCT1"        "IPCEF1"       "TIAM2"        "TULP4"       
##  [757] "TAGAP"        "SOD2"         "IGF2R"        "CCR6"        
##  [761] "DLL1"         "FAM120B"      "SUN1"         "GPR146"      
##  [765] "CARD11"       "AP5Z1"        "RBAK"         "GLCCI1"      
##  [769] "TSPAN13"      "HDAC9"        "RAPGEF5"      "NPY"         
##  [773] "KIAA0087"     "HOXA5"        "HOXA9"        "CREB5"       
##  [777] "HERPUD2"      "AOAH"         "ELMO1"        "YAE1D1"      
##  [781] "CDK13"        "SUGCT"        "STK17A"       "MRPS24"      
##  [785] "LINC00957"    "AEBP1"        "UPP1"         "FIGNL1"      
##  [789] "COBL"         "ZNF736"       "ZNF680"       "ZNF107"      
##  [793] "ZNF138"       "ERV3-1"       "ZNF92"        "TPST1"       
##  [797] "KCTD7"        "AUTS2"        "LIMK1"        "LAT2"        
##  [801] "NCF1"         "GTF2IRD2"     "GTF2IRD2B"    "TRIM73"      
##  [805] "HIP1"         "CCDC146"      "GSAP"         "GNAI1"       
##  [809] "CD36"         "TMEM243"      "ABCB4"        "ABCB1"       
##  [813] "RUNDC3B"      "STEAP4"       "GTPBP10"      "AKAP9"       
##  [817] "PEX1"         "SAMD9"        "SAMD9L"       "GNG11"       
##  [821] "CASD1"        "NPTX2"        "PTCD1"        "FAM200A"     
##  [825] "CYP3A5"       "GPC2"         "PILRA"        "ZCWPW1"      
##  [829] "PCOLCE"       "TFR2"         "TRIM56"       "CLDN15"      
##  [833] "PRKRIP1"      "ALKBH4"       "CCDC71L"      "PRKAR2B"     
##  [837] "DUS4L"        "DNAJB9"       "TMEM168"      "MDFIC"       
##  [841] "CAV1"         "FAM3C"        "ASB15"        "METTL2B"     
##  [845] "TSPAN33"      "NRF1"         "UBE2H"        "KLHDC10"     
##  [849] "TMEM209"      "AC016831.7"   "PLXNA4"       "BPGM"        
##  [853] "CALD1"        "TMEM140"      "PARP12"       "KDM7A"       
##  [857] "SLC37A3"      "EPHB6"        "ARHGEF5"      "TPK1"        
##  [861] "CNTNAP2"      "ZNF786"       "ZNF746"       "ZNF862"      
##  [865] "ATP6V0E2"     "ZNF775"       "LINC00996"    "GIMAP8"      
##  [869] "GIMAP7"       "GIMAP4"       "GIMAP6"       "GIMAP2"      
##  [873] "GIMAP1"       "KCNH2"        "PAXIP1-AS1"   "AC144652.1"  
##  [877] "INSIG1"       "RNF32"        "PTPRN2"       "IL3RA"       
##  [881] "P2RY8"        "CD99"         "TCEANC"       "TRAPPC2"     
##  [885] "OFD1"         "GPM6B"        "CA5B"         "ZRSR2"       
##  [889] "AP1S2"        "CNKSR2"       "SAT1"         "CYBB"        
##  [893] "MID1IP1"      "GPR82"        "KDM6A"        "KRBOX4"      
##  [897] "ZNF674-AS1"   "SLC9A7"       "CFP"          "TBC1D25"     
##  [901] "GATA1"        "PCSK1N"       "CCDC120"      "PRAF2"       
##  [905] "SYP"          "PPP1R3F"      "MAGEH1"       "USP51"       
##  [909] "KLF8"         "UBQLN2"       "ZXDA"         "ZC4H2"       
##  [913] "PJA1"         "DLG3"         "IL2RG"        "CXCR3"       
##  [917] "NAP1L2"       "CHIC1"        "TSIX"         "FTX"         
##  [921] "MAGEE1"       "TAF9B"        "CYSLTR1"      "P2RY10"      
##  [925] "ITM2A"        "CHM"          "NAP1L3"       "FAM133A"     
##  [929] "TRMT2B"       "BTK"          "ARMCX4"       "ARMCX1"      
##  [933] "ARMCX2"       "ZMAT1"        "TCEAL2"       "BEX5"        
##  [937] "ARMCX5"       "GPRASP1"      "GPRASP2"      "BEX1"        
##  [941] "BEX2"         "SLC25A53"     "MORC4"        "RBM41"       
##  [945] "TSC22D3"      "IL13RA1"      "XIAP"         "RAB33A"      
##  [949] "FAM122C"      "MOSPD1"       "ZNF75D"       "LDOC1"       
##  [953] "IDS"          "TMEM185A"     "MTMR1"        "PNMA3"       
##  [957] "ZNF275"       "TMEM187"      "GDI1"         "PLXNA3"      
##  [961] "MPP1"         "FBXO25"       "CLN8"         "ARHGEF10"    
##  [965] "KBTBD11"      "MYOM2"        "ANGPT2"       "PPP1R3B"     
##  [969] "MTMR9"        "BLK"          "CTSB"         "MTUS1"       
##  [973] "PSD3"         "CSGALNACT1"   "DOK2"         "PPP3CC"      
##  [977] "SORBS3"       "CCAR2"        "ENTPD4"       "ADAM28"      
##  [981] "EPHX2"        "NUGGC"        "PNOC"         "FZD3"        
##  [985] "DUSP4"        "DUSP26"       "RAB11FIP1"    "DDHD2"       
##  [989] "FGFR1"        "ANK1"         "AP3M2"        "RNF170"      
##  [993] "CEBPD"        "PLAG1"        "CHD7"         "PDE7A"       
##  [997] "LY96"         "TPD52"        "ZBTB10"       "PAG1"        
## [1001] "FABP5"        "E2F5"         "CA1"          "CA2"         
## [1005] "WWP1"         "TMEM64"       "OTUD6B"       "LRRC69"      
## [1009] "TMEM67"       "PLEKHF2"      "LAPTM4B"      "VPS13B"      
## [1013] "SPAG1"        "RNF19A"       "ANKRD46"      "NCALD"       
## [1017] "KLF10"        "BAALC"        "ANGPT1"       "TRPS1"       
## [1021] "SAMD12"       "ZHX2"         "ATAD2"        "FBXO32"      
## [1025] "TRIB1"        "PCAT1"        "TMEM71"       "ZFAT"        
## [1029] "PTP4A3"       "GLI4"         "RHPN1"        "ZC3H3"       
## [1033] "ZNF623"       "ZNF707"       "NRBP2"        "PLEC"        
## [1037] "PARP10"       "ADCK5"        "ZNF7"         "ZNF250"      
## [1041] "RFX3"         "CDC37L1"      "RANBP6"       "KDM4C"       
## [1045] "ZDHHC21"      "SNAPC3"       "MLLT3"        "KLHL9"       
## [1049] "ACO1"         "DDX58"        "NFX1"         "FAM219A"     
## [1053] "ENHO"         "GALT"         "IL11RA"       "CD72"        
## [1057] "SIT1"         "CCDC107"      "TPM2"         "GBA2"        
## [1061] "RGP1"         "NPR2"         "TMEM8B"       "RECK"        
## [1065] "GNE"          "PAX5"         "ZCCHC7"       "TRMT10B"     
## [1069] "CBWD5"        "CBWD3"        "FAM122A"      "KLF9"        
## [1073] "ABHD17B"      "ALDH1A1"      "NMRK1"        "PSAT1"       
## [1077] "TLE1"         "GKAP1"        "NAA35"        "SEMA4D"      
## [1081] "GADD45G"      "AUH"          "NFIL3"        "ZNF484"      
## [1085] "FGD3"         "SUSD3"        "ERCC6L2"      "HABP4"       
## [1089] "ZNF782"       "HEMGN"        "NR4A3"        "STX17"       
## [1093] "TMEM246"      "ABCA1"        "SLC44A1"      "KLF4"        
## [1097] "ZNF483"       "UGCG"         "ZFP37"        "TNFSF8"      
## [1101] "MEGF9"        "GSN"          "ZBTB6"        "STRBP"       
## [1105] "CRB2"         "SCAI"         "HSPA5"        "ZBTB43"      
## [1109] "RALGPS1"      "SH2D3C"       "ST6GALNAC6"   "PIP5KL1"     
## [1113] "FAM102A"      "SPTAN1"       "FAM78A"       "POMT1"       
## [1117] "RAPGEF1"      "NTNG2"        "TTF1"         "TSC1"        
## [1121] "CACFD1"       "SLC2A6"       "SARDH"        "FCN1"        
## [1125] "EGFL7"        "CLIC3"        "FUT7"         "NPDC1"       
## [1129] "LRRC26"       "EXD3"         "NOXA1"        "NSMF"        
## [1133] "PNPLA7"       "KLF6"         "ANKRD16"      "IL2RA"       
## [1137] "TAF3"         "GATA3"        "USP6NL"       "DHTKD1"      
## [1141] "CAMK1D"       "OPTN"         "FRMD4A"       "FAM107B"     
## [1145] "DCLRE1C"      "NMT2"         "PLXDC2"       "OTUD1"       
## [1149] "ANKRD26"      "SVIL"         "ZEB1"         "CCDC7"       
## [1153] "ZNF25"        "ZNF33B"       "CXCL12"       "ALOX5"       
## [1157] "MARCH8"       "ANK3"         "ARID5B"       "HERC4"       
## [1161] "RUFY2"        "SLC25A16"     "TET1"         "SRGN"        
## [1165] "SUPV3L1"      "AIFM2"        "PRF1"         "DDIT4"       
## [1169] "MSS51"        "SAMD8"        "TSPAN14"      "SH2D4B"      
## [1173] "IFIT2"        "IFIT3"        "IFIT1"        "IFIT5"       
## [1177] "LINC00865"    "BLNK"         "ZFYVE27"      "R3HCC1L"     
## [1181] "SEC31B"       "SFXN3"        "NFKB2"        "ITPRIP"      
## [1185] "ADD3"         "MXI1"         "GPAM"         "AFAP1L2"     
## [1189] "PDZD8"        "RAB11FIP2"    "GRK5"         "PLEKHA1"     
## [1193] "FAM24B"       "LHPP"         "PTPRE"        "LRRC27"      
## [1197] "ADAM8"        "PAOX"         "MTG1"         "BET1L"       
## [1201] "IFITM2"       "IFITM3"       "IRF7"         "SCT"         
## [1205] "TMEM80"       "TNNI2"        "TRIM68"       "HBB"         
## [1209] "HBD"          "HBG2"         "DNHD1"        "RIC3"        
## [1213] "STK33"        "TMEM41B"      "ZNF143"       "SWAP70"      
## [1217] "ZBED5"        "RRAS2"        "PIK3C2A"      "IGSF22"      
## [1221] "FANCF"        "MPPED2"       "FBXO3"        "CAT"         
## [1225] "PRR5L"        "TRAF6"        "RAG1"         "RAG2"        
## [1229] "CD82"         "TP53I11"      "CRY2"         "MDK"         
## [1233] "HARBI1"       "SPI1"         "KBTBD4"       "C1QTNF4"     
## [1237] "PTPRJ"        "MPEG1"        "MS4A3"        "MS4A6A"      
## [1241] "MS4A4A"       "MS4A7"        "MS4A1"        "CYB561A3"    
## [1245] "FADS3"        "AHNAK"        "TTC9C"        "RARRES3"     
## [1249] "PLA2G16"      "TRPT1"        "PPP1R14B"     "PYGM"        
## [1253] "MAP4K2"       "CDC42BPG"     "EHD1"         "ATG2A"       
## [1257] "PPP2R5B"      "NAALADL1"     "TM7SF2"       "SYVN1"       
## [1261] "SLC25A45"     "NEAT1"        "LTBP3"        "PACS1"       
## [1265] "KLC2"         "CD248"        "CTSF"         "ANKRD13D"    
## [1269] "TBC1D10C"     "CARNS1"       "CABP4"        "CDK2AP2"     
## [1273] "ACY3"         "UNC93B1"      "TCIRG1"       "ORAOV1"      
## [1277] "LRTOMT"       "STARD10"      "UCP2"         "UCP3"        
## [1281] "P4HA3"        "PGM2L1"       "XRRA1"        "INTS4"       
## [1285] "RAB30-AS1"    "CCDC81"       "PRSS23"       "MED17"       
## [1289] "ANKRD49"      "MAML2"        "BIRC3"        "DYNC2H1"     
## [1293] "KBTBD3"       "CWF19L2"      "EXPH5"        "POU2AF1"     
## [1297] "BCO2"         "ZBTB16"       "REXO2"        "APOA1"       
## [1301] "PCSK7"        "FXYD2"        "MPZL3"        "CD3E"        
## [1305] "BCL9L"        "CCDC84"       "MCAM"         "UBASH3B"     
## [1309] "CRTAM"        "ESAM"         "FEZ1"         "HYLS1"       
## [1313] "ETS1"         "TMEM45B"      "ACAD8"        "ERC1"        
## [1317] "FBXL14"       "ITFG2"        "PARP11"       "VWF"         
## [1321] "CD9"          "CD27"         "VAMP1"        "IFFO1"       
## [1325] "LAG3"         "CLSTN3"       "CLEC4C"       "SLC2A3"      
## [1329] "NECAP1"       "CLEC4A"       "LINC00937"    "RIMKLB"      
## [1333] "PHC1"         "KLRB1"        "CLEC2D"       "CD69"        
## [1337] "CLEC2B"       "CLEC12A"      "CLEC9A"       "GABARAPL1"   
## [1341] "KLRD1"        "YBX3"         "PRR4"         "TAS2R14"     
## [1345] "TAS2R30"      "LRP6"         "DUSP16"       "APOLD1"      
## [1349] "EMP1"         "ATF7IP"       "HIST4H4"      "ERP27"       
## [1353] "MGST1"        "PYROXD1"      "CAPRIN2"      "AMN1"        
## [1357] "IRAK4"        "TWF1"         "SLC38A1"      "AMIGO2"      
## [1361] "RAPGEF3"      "HDAC7"        "SENP1"        "ZNF641"      
## [1365] "RND1"         "FKBP11"       "LMBR1L"       "PRPF40B"     
## [1369] "FMNL3"        "BCDIN3D"      "CERS5"        "POU6F1"      
## [1373] "BIN2"         "NR4A1"        "CSAD"         "ITGB7"       
## [1377] "CALCOCO1"     "TESPA1"       "RDH5"         "GDF11"       
## [1381] "DGKA"         "IKZF4"        "ZC3H10"       "COQ10A"      
## [1385] "PAN2"         "IL23A"        "HSD17B6"      "LRP1"        
## [1389] "TSPAN31"      "AVIL"         "SLC16A7"      "FAM19A2"     
## [1393] "MON2"         "LEMD3"        "MSRB3"        "DYRK2"       
## [1397] "SLC35E3"      "FRS2"         "BEST3"        "RAB3IP"      
## [1401] "THAP2"        "BBS10"        "ZDHHC17"      "PAWR"        
## [1405] "METTL25"      "CEP290"       "DUSP6"        "POC1B"       
## [1409] "BTG1"         "SOCS2"        "HSP90B1"      "HCFC2"       
## [1413] "EID3"         "TCP11L2"      "RIC8B"        "CRY1"        
## [1417] "TCTN1"        "SH2B3"        "ACAD10"       "ALDH2"       
## [1421] "OAS2"         "DTX1"         "SLC8B1"       "HRK"         
## [1425] "FBXO21"       "OASL"         "MORN3"        "SETD1B"      
## [1429] "WDR66"        "BCL7A"        "MLXIP"        "DIABLO"      
## [1433] "HIP1R"        "PITPNM2"      "RILPL1"       "SLC15A4"     
## [1437] "MMP17"        "ULK1"         "ZNF605"       "ZNF140"      
## [1441] "ZNF891"       "ZNF268"       "ZMYM5"        "IFT88"       
## [1445] "PABPC3"       "FLT3"         "FLT1"         "SLC46A3"     
## [1449] "UBL3"         "LINC00544"    "LINC00426"    "USPL1"       
## [1453] "ALOX5AP"      "NBEA"         "FOXO1"        "KBTBD6"      
## [1457] "KBTBD7"       "MTRF1"        "RGCC"         "DGKH"        
## [1461] "AKAP11"       "TSC22D1"      "LRCH1"        "RCBTB2"      
## [1465] "SETDB2"       "TRIM13"       "KCNRG"        "INTS6"       
## [1469] "TDRD3"        "PCDH9"        "PIBF1"        "KLF5"        
## [1473] "KLF12"        "LMO7"         "KCTD12"       "CLN5"        
## [1477] "POU4F1"       "MBNL2"        "GPR18"        "GPR183"      
## [1481] "ERCC5"        "TNFSF13B"     "IRS2"         "MCF2L"       
## [1485] "GAS6"         "RASA3"        "RNASE6"       "RNASE3"      
## [1489] "RNASE2"       "NDRG2"        "RAB2B"        "SLC7A7"      
## [1493] "LRP10"        "CEBPE"        "PPP1R3E"      "CMTM5"       
## [1497] "NRL"          "IRF9"         "TM9SF1"       "RIPK3"       
## [1501] "CBLN3"        "KHNYN"        "CTSG"         "GZMB"        
## [1505] "STXBP6"       "AP4S1"        "NUBPL"        "ARHGAP5"     
## [1509] "CLEC14A"      "KLHL28"       "PRPF39"       "MIS18BP1"    
## [1513] "VCPKMT"       "GNG2"         "PTGDR"        "PTGER2"      
## [1517] "DDHD1"        "TMEM260"      "DACT1"        "DAAM1"       
## [1521] "L3HYPDH"      "PRKCH"        "HIF1A"        "SYNE2"       
## [1525] "ESR2"         "AKAP5"        "RAB15"        "RAD51B"      
## [1529] "ZFP36L1"      "ACTN1"        "DCAF5"        "SYNJ2BP"     
## [1533] "TTC9"         "ELMSAN1"      "ABCD4"        "IRF2BPL"     
## [1537] "TC2N"         "FBLN5"        "TRIP11"       "LGMN"        
## [1541] "MOAP1"        "BTBD7"        "SYNE3"        "TCL1B"       
## [1545] "TCL1A"        "ATG2B"        "CYP46A1"      "EVL"         
## [1549] "MEG3"         "PPP2R5C"      "WDR20"        "TNFAIP2"     
## [1553] "CKB"          "PPP1R13B"     "PLD4"         "CRIP2"       
## [1557] "CRIP1"        "NIPA1"        "SNRPN"        "PWAR6"       
## [1561] "PGBD4"        "SLC12A6"      "RASGRP1"      "SRP14-AS1"   
## [1565] "BAHD1"        "MAPKBP1"      "CAPN3"        "STARD9"      
## [1569] "EPB42"        "MAP1A"        "CATSPER2"     "PATL2"       
## [1573] "TRIM69"       "DUOX1"        "SECISBP2L"    "FGF7"        
## [1577] "ATP8B4"       "HDC"          "GABPB1"       "TRPM7"       
## [1581] "DMXL2"        "TMOD2"        "GNB5"         "FAM214A"     
## [1585] "LINC00926"    "RORA"         "TPM1"         "FBXL22"      
## [1589] "SNX22"        "PPIB"         "PIF1"         "ANKDD1A"     
## [1593] "MAP2K5"       "CORO2B"       "STOML1"       "ARID3B"      
## [1597] "NEIL1"        "SCAPER"       "PSTPIP1"      "BCL2A1"      
## [1601] "IL16"         "WHAMM"        "ZSCAN2"       "WDR73"       
## [1605] "PDE8A"        "SEMA4B"       "MCTP2"        "ASB7"        
## [1609] "HBA1"         "NHLRC4"       "NARFL"        "LMF1"        
## [1613] "TPSAB1"       "UNKL"         "CCDC154"      "NPW"         
## [1617] "PRSS21"       "FLYWCH1"      "ZNF200"       "ZNF263"      
## [1621] "ZNF75A"       "DNASE1"       "VASN"         "ANKS3"       
## [1625] "ZNF500"       "PPL"          "ATF7IP2"      "CIITA"       
## [1629] "SOCS1"        "LITAF"        "SNN"          "TXNDC11"     
## [1633] "SNX29"        "MYH11"        "COQ7"         "ACSM3"       
## [1637] "TMEM159"      "IGSF6"        "NPIPB4"       "SDR42E2"     
## [1641] "NPIPB5"       "GGA2"         "SBK1"         "RABEP2"      
## [1645] "CD19"         "LAT"          "PRRT2"        "ZNF771"      
## [1649] "ITGAL"        "ZNF688"       "ZNF785"       "AHSP"        
## [1653] "ZNF720"       "AKTIP"        "CES1"         "BBS2"        
## [1657] "MT1E"         "MT1F"         "MT1X"         "HERPUD1"     
## [1661] "NLRC5"        "CPNE2"        "CCDC102A"     "TEPP"        
## [1665] "CMTM2"        "CES4A"        "ACD"          "GFOD2"       
## [1669] "SLC7A6"       "SLC7A6OS"     "ZFP90"        "SNTB2"       
## [1673] "CLEC18A"      "DDX19A"       "CMTR2"        "ZNF19"       
## [1677] "ATXN1L"       "ZNF821"       "ADAT1"        "MAF"         
## [1681] "TLDC1"        "COTL1"        "KLHL36"       "CRISPLD2"    
## [1685] "IRF8"         "CYBA"         "ZNF778"       "VPS9D1"      
## [1689] "GAS8"         "VPS53"        "CRK"          "INPP5K"      
## [1693] "SLC43A2"      "MIR22HG"      "SERPINF1"     "SMYD4"       
## [1697] "ZZEF1"        "CYB5D2"       "SPNS3"        "CXCL16"      
## [1701] "GP1BA"        "CAMTA2"       "ZNF594"       "SCIMP"       
## [1705] "NLRP1"        "XAF1"         "RNASEK"       "SLC16A13"    
## [1709] "SLC16A11"     "ACAP1"        "ZBTB4"        "TNFSF12"     
## [1713] "CD68"         "KDM6B"        "PER1"         "TMEM107"     
## [1717] "LINC00324"    "CTC1"         "CCDC42"       "PIK3R5"      
## [1721] "MYH3"         "ADPRM"        "ARHGAP44"     "HS3ST3B1"    
## [1725] "TRPV2"        "CCDC144A"     "FLCN"         "MED9"        
## [1729] "RASD1"        "TOM1L2"       "GRAP"         "GRAPL"       
## [1733] "EPN2"         "AKAP10"       "LYRM9"        "ALDOC"       
## [1737] "NEK8"         "SEZ6"         "ABHD15"       "CRLF3"       
## [1741] "TEFM"         "RAB11FIP4"    "LRRC37B"      "SLFN5"       
## [1745] "MMP28"        "CCL5"         "CCL3"         "CCL4"        
## [1749] "SYNRG"        "LINC00672"    "PLXDC1"       "FBXL20"      
## [1753] "CDK12"        "TCAP"         "ERBB2"        "IKZF3"       
## [1757] "GSDMB"        "CCR7"         "JUP"          "KLHL11"      
## [1761] "ATP6V0A1"     "CCR10"        "EZH1"         "RUNDC1"      
## [1765] "LINC00910"    "GRN"          "ITGA2B"       "NMT1"        
## [1769] "HEXIM1"       "LRRC37A"      "LRRC37A2"     "EFCAB13"     
## [1773] "LRRC46"       "SKAP1"        "HOXB2"        "ZNF652"      
## [1777] "NGFR"         "FAM117A"      "ITGA3"        "TOB1"        
## [1781] "HLF"          "NOG"          "DGKE"         "SCPEP1"      
## [1785] "MSI2"         "RNF43"        "MTMR4"        "YPEL2"       
## [1789] "TUBD1"        "BCAS3"        "CYB561"       "ACE"         
## [1793] "CD79B"        "MILR1"        "CEP95"        "SMURF2"      
## [1797] "LRRC37A3"     "RGS9"         "PITPNC1"      "SDK2"        
## [1801] "RAB37"        "ARMC7"        "MYO15B"       "RECQL5"      
## [1805] "UNK"          "QRICH2"       "RHBDF2"       "CYGB"        
## [1809] "PRCD"         "MXRA7"        "TNRC6C"       "SOCS3"       
## [1813] "CYTH1"        "LGALS3BP"     "CBX4"         "SGSH"        
## [1817] "HEXDC"        "YES1"         "METTL4"       "MYOM1"       
## [1821] "TGIF1"        "ZBTB14"       "RAB12"        "RAB31"       
## [1825] "LDLRAD4"      "NPC1"         "RNF125"       "ZNF397"      
## [1829] "ZSCAN30"      "SETBP1"       "SMAD7"        "SMAD4"       
## [1833] "MEX3C"        "RAB27B"       "TCF4"         "ATP8B1"      
## [1837] "MALT1"        "ZNF532"       "PMAIP1"       "RNF152"      
## [1841] "SERPINB2"     "SERPINB10"    "SERPINB8"     "CDH7"        
## [1845] "DSEL"         "CCDC102B"     "LINC00909"    "ZNF407"      
## [1849] "HSBP1L1"      "TBC1D20"      "FAM110A"      "ZNF343"      
## [1853] "OXT"          "AVP"          "UBOX5"        "FASTKD5"     
## [1857] "LZTS3"        "GPCPD1"       "BTBD3"        "MACROD2"     
## [1861] "KIF16B"       "DZANK1"       "NAPB"         "CST7"        
## [1865] "ACSS1"        "ZNF337"       "ID1"          "CDK5RAP1"    
## [1869] "CBFA2T2"      "ACTL10"       "MAP1LC3A"     "MYH7B"       
## [1873] "SPAG4"        "DLGAP4"       "MYL9"         "NDRG3"       
## [1877] "SAMHD1"       "PPP1R16B"     "PLCG1"        "ZHX3"        
## [1881] "L3MBTL1"      "MYBL2"        "TOX2"         "TTPAL"       
## [1885] "PKIG"         "ADA"          "PCIF1"        "ZNF335"      
## [1889] "ZMYND8"       "ZNFX1"        "CEBPB"        "BCAS4"       
## [1893] "MOCS3"        "KCNG1"        "NFATC2"       "CASS4"       
## [1897] "PMEPA1"       "VAPB"         "CTSZ"         "OSBPL2"      
## [1901] "PTK6"         "HELZ2"        "STMN3"        "UCKL1"       
## [1905] "PCMTD2"       "MADCAM1"      "PRSS57"       "AZU1"        
## [1909] "PRTN3"        "ELANE"        "CFD"          "ARID3A"      
## [1913] "SBNO2"        "MIDN"         "LINGO3"       "GADD45B"     
## [1917] "GNG7"         "S1PR4"        "TBXA2R"       "APBA3"       
## [1921] "PIAS4"        "SHD"          "SEMA6B"       "TNFAIP8L1"   
## [1925] "DPP9"         "ARRDC5"       "KDM4B"        "PTPRS"       
## [1929] "TINCR"        "HSD11B1L"     "VMAC"         "CAPS"        
## [1933] "ACER1"        "TNFSF14"      "SH2D3A"       "ZNF557"      
## [1937] "PCP2"         "STXBP2"       "RETN"         "EVI5L"       
## [1941] "CERS4"        "PRAM1"        "ZNF699"       "ZNF559"      
## [1945] "ZNF266"       "ZNF426"       "ATG4D"        "SLC44A2"     
## [1949] "LDLR"         "KANK2"        "DOCK6"        "SWSAP1"      
## [1953] "ZNF627"       "ZNF441"       "ZNF439"       "ZNF844"      
## [1957] "ZNF136"       "ZNF44"        "ZNF564"       "ZNF791"      
## [1961] "WDR83"        "HOOK2"        "PRDX2"        "KLF1"        
## [1965] "IER2"         "CACNA1A"      "CCDC130"      "DCAF15"      
## [1969] "RFX1"         "IL27RA"       "GIPC1"        "DNAJB1"      
## [1973] "ZNF333"       "RASAL3"       "PGLYRP2"      "HSH2D"       
## [1977] "KLF2"         "SIN3B"        "F2RL3"        "FAM129C"     
## [1981] "FCHO1"        "JAK3"         "ARRDC2"       "IFI30"       
## [1985] "LRRC25"       "SLC25A42"     "SUGP1"        "ZNF101"      
## [1989] "ZNF14"        "ZNF506"       "ZNF253"       "ZNF682"      
## [1993] "ZNF486"       "ZNF626"       "ZNF430"       "ZNF431"      
## [1997] "ZNF708"       "ZNF493"       "ZNF429"       "ZNF100"      
## [2001] "ZNF91"        "ZNF675"       "ZNF681"       "ZNF254"      
## [2005] "LINC00662"    "ZNF507"       "ZNF181"       "ZNF30"       
## [2009] "GRAMD1A"      "FXYD7"        "LSR"          "CD22"        
## [2013] "DMKN"         "KMT2B"        "NFKBID"       "HCST"        
## [2017] "TYROBP"       "ZFP14"        "ZFP82"        "ZNF566"      
## [2021] "ZNF382"       "ZNF461"       "ZNF567"       "ZNF790"      
## [2025] "ZNF345"       "ZNF568"       "ZNF420"       "ZNF585A"     
## [2029] "ZNF585B"      "ZNF383"       "ZNF527"       "ZNF569"      
## [2033] "ZNF793"       "ZNF571"       "ZFP30"        "ZNF781"      
## [2037] "ZNF573"       "PPP1R14A"     "CATSPERG"     "FAM98C"      
## [2041] "CAPN12"       "EID2B"        "CLC"          "ZNF780B"     
## [2045] "SERTAD1"      "BLVRB"        "RAB4B"        "CEACAM21"    
## [2049] "CD79A"        "ARHGEF1"      "ATP1A3"       "POU2F2"      
## [2053] "LIPE"         "ZNF575"       "ZNF404"       "ZNF224"      
## [2057] "ZNF234"       "ZNF226"       "APOE"         "APOC1"       
## [2061] "RELB"         "PPP1R37"      "BLOC1S3"      "PPP1R13L"    
## [2065] "FOSB"         "PPM1N"        "OPA3"         "EML2"        
## [2069] "PTGIR"        "PRKD2"        "BBC3"         "LMTK3"       
## [2073] "SPHK2"        "CA11"         "HSD17B14"     "SLC6A16"     
## [2077] "CD37"         "FLT3LG"       "PRRG2"        "RRAS"        
## [2081] "TBC1D17"      "SPIB"         "CLEC11A"      "NKG7"        
## [2085] "SIGLEC10"     "FPR1"         "ZNF577"       "ZNF649"      
## [2089] "ZNF350"       "ZNF615"       "ZNF432"       "ZNF836"      
## [2093] "ZNF766"       "ZNF610"       "ZNF880"       "ZNF808"      
## [2097] "ZNF701"       "ZNF83"        "ZNF611"       "ZNF600"      
## [2101] "ZNF468"       "ZNF665"       "ZNF677"       "ZNF813"      
## [2105] "MYADM"        "LENG1"        "LILRB2"       "LILRA5"      
## [2109] "LILRA4"       "LAIR2"        "KIR3DX1"      "LILRB4"      
## [2113] "TNNT1"        "UBE2S"        "ZNF865"       "ZNF784"      
## [2117] "ZNF444"       "ZNF582-AS1"   "ZNF583"       "ZNF667"      
## [2121] "ZNF264"       "ZNF543"       "ZNF548"       "ZNF17"       
## [2125] "ZNF419"       "ZNF773"       "ZNF211"       "ZNF154"      
## [2129] "ZNF671"       "ZNF586"       "ZNF552"       "ZNF587"      
## [2133] "ZNF418"       "ZNF606"       "ZSCAN18"      "ZNF329"      
## [2137] "ZNF274"       "ZNF544"       "ZNF837"       "ZNF446"      
## [2141] "MZF1"         "UTY"          "IL17RA"       "LINC00528"   
## [2145] "USP18"        "CLDN5"        "SDF2L1"       "YPEL1"       
## [2149] "VPREB1"       "BCR"          "IGLL1"        "RGL4"        
## [2153] "VPREB3"       "MMP11"        "SLC2A11"      "SGSM1"       
## [2157] "KIAA1671"     "LRP5L"        "HPS4"         "MIAT"        
## [2161] "KREMEN1"      "OSM"          "SLC35E4"      "PIK3IP1"     
## [2165] "TIMP3"        "HMOX1"        "APOL6"        "APOL3"       
## [2169] "APOL2"        "CSF2RB"       "KCTD17"       "CYTH4"       
## [2173] "H1F0"         "PICK1"        "MAFF"         "CSNK1E"      
## [2177] "APOBEC3G"     "CBX7"         "SYNGR1"       "XPNPEP3"     
## [2181] "CYP2D6"       "TCF20"        "CELSR1"       "TBC1D22A"    
## [2185] "BRD1"         "PIM3"         "PPP6R2"       "SBF1"        
## [2189] "ODF3B"        "NRIP1"        "MIR155HG"     "LTN1"        
## [2193] "ERG"          "LINC00114"    "MX2"          "MX1"         
## [2197] "UMODL1"       "SLC37A1"      "PDE9A"        "ICOSLG"      
## [2201] "AIRE"         "ITGB2"        "COL6A2"       "DIP2A"

#Use softmax regression for viewmaster. We will use the Greenleaf lab’s MPAL healthy bone marrow cell annotations and transfer them to Human Cell Atals of bone marrow

view<-viewmaster(ref_cds  = mpal, query_cds = hca, ref_celldata_col = "BioClassification", selected_genes = vg, verbose=T, FUNC = "softmax_regression", tf_idf = F)

plot_cells(view, color_cells_by = "smr_celltype", label_cell_groups = F)+scale_color_manual(values = sfc(11))

#logistic regression matrix

hca_seu<-monocle3_to_seurat(hca)
mpal_seu<-monocle3_to_seurat(mpal, mon_rd = "UMAP")

log_mat<-log_reg_matrix(trainDat = mpal_seu, testDat = hca_seu, trainClass = "BioClassification", testClass = "cell_annotation", downsample = 500)

testDat<- loadTrainingData(hca_seu)

clusterPreds = apply(log_mat,2,function(e) sapply(split(e,testDat$mDat[["cell_annotation"]]),mean))

#Convet to percentages
clusterPreds = (1+exp(-clusterPreds))**-1

pheatmap(clusterPreds, cluster_cols=T,cluster_rows = T ,col = ArchR::paletteContinuous("coolwarm", n=10, reverse = F), border_color = "black")

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